pal.coalescent
Class ConstExpConst

java.lang.Object
  pal.coalescent.DemographicModel
      pal.coalescent.ConstantPopulation
          pal.coalescent.ExponentialGrowth
              pal.coalescent.ConstExpGrowth
                  pal.coalescent.ConstExpConst

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units

public class ConstExpConst
extends ConstExpGrowth
implements Report, Parameterized, java.io.Serializable

This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day. (Parameters: N0=present-day population size; r=growth rate; alpha: ratio of population sizes). or (Parameters: N0=present-day population size; r=growth rate; N1: pre-growth ancestral population size). This model is nested with the exponential-growth model (alpha -> 0 and tx -> 0).

Version:

$Id: ConstExpConst.java,v 1.2 2002/02/16 00:51:43 alexi Exp $

Author:

Alexei Drummond, Andrew Rambaut

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

double	tx time of end of exponential growth
double	txSE standard error of time of growth

Fields inherited from class pal.coalescent.ConstExpGrowth

alpha, ALPHA_PARAMETERIZATION, alphaSE, LX_PARAMETERIZATION, N1, N1_PARAMETERIZATION, N1SE, parameterization

Fields inherited from class pal.coalescent.ExponentialGrowth

r, rSE

Fields inherited from class pal.coalescent.ConstantPopulation

N0, N0SE

Fields inherited from class pal.coalescent.DemographicModel

fo

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

ConstExpConst(double size, double growth, double ancestral, double timeX, int units, int parameterization)
Construct demographic model of constexpconst population.

ConstExpConst(int units, int parameterization)
Construct demographic model with default settings.

Method Summary

java.lang.Object	clone() Makes a copy of this demographic model.
double	getDefaultValue(int k) get default value of parameter
double	getDemographic(double t) Gets the value of the demographic function N(t) at time t.
double	getGrowthPhaseDuration()
double	getIntensity(double t) Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
double	getInverseIntensity(double x) Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
double	getLowerLimit(int k) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int k) get model parameter
double	getTimeX()
double	getTransitionTime() Gets the time of transition from initial constant phase to exponential phase.
double	getUpperLimit(int k) get upper parameter limit
static void	main(java.lang.String[] args)
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	setParameter(double value, int k) set model parameter
void	setParameterSE(double value, int k) set standard errors for model parameter
void	setTimeX(double timeX)
java.lang.String	toString()

Methods inherited from class pal.coalescent.ConstExpGrowth

calculateRFromLx, getAncestral, getAncestralN0, getGrowthParam, getGrowthRate, getParameterization, isLxParameterized, isN1Parameterized, setAncestral, setGrowthParam, setGrowthPhaseDuration, setParameterization

Methods inherited from class pal.coalescent.ExponentialGrowth

getSummaryTypes, getSummaryValue

Methods inherited from class pal.coalescent.ConstantPopulation

getN0

Methods inherited from class pal.coalescent.DemographicModel

computeLogLikelihood, computeLogLikelihood, getIntegral, getLogL, getSimulatedInterval, getUnits, setLogL, setUnits, testConsistency

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

tx

public double tx

time of end of exponential growth

txSE

public double txSE

standard error of time of growth

Constructor Detail

ConstExpConst

public ConstExpConst(int units,
                     int parameterization)

Construct demographic model with default settings.

ConstExpConst

public ConstExpConst(double size,
                     double growth,
                     double ancestral,
                     double timeX,
                     int units,
                     int parameterization)

Construct demographic model of constexpconst population.

Method Detail

clone

public java.lang.Object clone()

Makes a copy of this demographic model.

Overrides:

clone in class ConstExpGrowth

getTransitionTime

public double getTransitionTime()

Gets the time of transition from initial constant phase to exponential phase.

Overrides:

getTransitionTime in class ConstExpGrowth

getGrowthPhaseDuration

public double getGrowthPhaseDuration()

Overrides:

getGrowthPhaseDuration in class ConstExpGrowth

Returns:

the duration of the growth phase

getTimeX

public double getTimeX()

Returns:

the time at which the modern constant pop size gives way to exponential phase.

setTimeX

public void setTimeX(double timeX)

getDemographic

public double getDemographic(double t)

Description copied from class: DemographicModel

Gets the value of the demographic function N(t) at time t.

Overrides:

getDemographic in class ConstExpGrowth

Returns:

the population size at time t.

getIntensity

public double getIntensity(double t)

Description copied from class: DemographicModel

Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).

Overrides:

getIntensity in class ConstExpGrowth

Returns:

the integral of 1 / N(t) from 0 to t.

getInverseIntensity

public double getInverseIntensity(double x)

Description copied from class: DemographicModel

Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).

Overrides:

getInverseIntensity in class ConstExpGrowth

Returns:

the time for the given intensity.

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Overrides:

getNumParameters in class ConstExpGrowth

Returns:

number of parameters

getParameter

public double getParameter(int k)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Overrides:

getParameter in class ConstExpGrowth

Parameters:

k - parameter number

Returns:

parameter value

getUpperLimit

public double getUpperLimit(int k)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Overrides:

getUpperLimit in class ConstExpGrowth

Parameters:

k - parameter number

Returns:

upper bound

getLowerLimit

public double getLowerLimit(int k)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Overrides:

getLowerLimit in class ConstExpGrowth

Parameters:

k - parameter number

Returns:

lower bound

getDefaultValue

public double getDefaultValue(int k)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Overrides:

getDefaultValue in class ConstExpGrowth

Parameters:

k - parameter number

Returns:

default value

setParameter

public void setParameter(double value,
                         int k)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Overrides:

setParameter in class ConstExpGrowth

Parameters:

value - parameter value

k - parameter number

setParameterSE

public void setParameterSE(double value,
                           int k)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Overrides:

setParameterSE in class ConstExpGrowth

Parameters:

value - standard error of parameter value

k - parameter number

toString

public java.lang.String toString()

Overrides:

toString in class ConstExpGrowth

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Overrides:

report in class ConstExpGrowth

Parameters:

out - output stream

main

public static void main(java.lang.String[] args)